Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.58 kDa 
• Atom Count: 660 
• Residue Count: 76 
• Unique protein chains: 1

1UBQ

STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION

• DOI: 10.2210/pdb1UBQ/pdb
• BMRB: 5387

• Classification: CHROMOSOMAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1987-01-02 Released: 1987-04-16 
• Deposition Author(s): Vijay-Kumar, S., Bugg, C.E., Cook, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.176 

Literature

Structure of ubiquitin refined at 1.8 A resolution.

Vijay-Kumar, S., Bugg, C.E., Cook, W.J.

(1987) J Mol Biol 194: 531-544

• PubMed: 3041007 
• DOI: 10.1016/0022-2836(87)90679-6
• Primary Citation of Related Structures:  
  1UBQ


• PubMed Abstract: 
  

The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.5 degrees, respectively. A total of 58 water molecules per molecule of ubiquitin are included in the final model. The last four residues in the molecule appear to have partial occupancy or large thermal motion. The overall structure of ubiquitin is extremely compact and tightly hydrogen-bonded; approximately 87% of the polypeptide chain is involved in hydrogen-bonded secondary structure. Prominent secondary structural features include three and one-half turns of alpha-helix, a short piece of 3(10)-helix, a mixed beta-sheet that contains five strands, and seven reverse turns. There is a marked hydrophobic core formed between the beta-sheet and alpha-helix. The molecule features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns.

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Related Citations: 

• Comparison of the Three-Dimensional Structures of Human, Yeast, and Oat Ubiquitin
  Vijay-Kumar, S., Bugg, C.E., Wilkinson, K.D., Vierstra, R.D., Hatfield, P.M., Cook, W.J.
  (1987) J Biol Chem 262: 6396

• Three-Dimensional Structure of Ubiquitin at 2.8 Angstroms Resolution
  Vijay-Kumar, S., Bugg, C.E., Wilkinson, K.D., Cook, W.J.
  (1985) Proc Natl Acad Sci U S A 82: 3582

• Crystallization and Preliminary X-Ray Investigation of Ubiquitin, a Non-Histone Chromosomal Protein
  Cook, W.J., Suddath, F.L., Bugg, C.E., Goldstein, G.
  (1979) J Mol Biol 130: 353

• Molecular Conservation of 74 Amino Acid Sequence of Ubiquitin between Cattle and Man
  Schlesinger, D.H., Goldstein, G.
  (1975) Nature 255: 423

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Organizational Affiliation: 

Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235-9050, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.84	α = 90
b = 42.77	β = 90
c = 28.95	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1987-01-02 
• Released Date: 1987-04-16 
Deposition Author(s): Vijay-Kumar, S., Bugg, C.E., Cook, W.J.

Revision History 

• Version 1.0: 1987-04-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance